Pulmonary arterial hypertension (PAH) occurs in approximately 15 % of patients with systemic sclerosis (SSc). Annual screening with pulmonary function tests (PFT) is recommended to help identify those patients at risk of PAH. We have noted that patients with SSc who carry anti-centromere autoantibodies (ACA) often have PFT abnormalities, in the absence of clinical evidence of PAH. To evaluate this further, we undertook a retrospective case-control study evaluating PFT results in patients with SSc in whom pulmonary complications have neither been diagnosed nor suspected. Patients were divided according to ACA carriage and groups compared for PFT results. The median forced vital capacity (FVC) was higher in ACA-positive patients (106 vs. 93 %, p = 0.004). The gas transfer factor (TLco) was significantly lower in the ACA group (62.5 vs. 71 %, p = 0.013). The resulting FVC:TLco was significantly higher for ACA-positive vs. ACA-negative patients with SSc (1.70 vs. 1.29, p < 0.001). Our findings suggest patients carrying ACA, without established or suspected pulmonary complications, have PFT abnormalities consistent with indolent increased pulmonary vascular resistance despite the majority of such patients not subsequently developing PAH. The long-term sequelae of PFT abnormalities in those patients with ACA who do not subsequently develop PAH are unknown.